To cite package ‘ShortRead’ in publications use:

  M. Morgan, S. Anders, M. Lawrence, P. Aboyoun, H. Pag\`es, and R.
  Gentleman (2009): "ShortRead: a Bioconductor package for input,
  quality assessment and exploration of high-throughput sequence data".
  Bioinformatics 25:2607-2608.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {{ShortRead}: a {B}ioconductor package for input, quality assessment and exploration of high-throughput sequence data},
    author = {Martin Morgan and Simon Anders and Michael Lawrence and Patrick Aboyoun and Herv\'e Pag\`es and Robert Gentleman},
    year = {2009},
    journal = {Bioinformatics},
    volume = {25},
    pages = {2607-2608},
    doi = {10.1093/bioinformatics/btp450},
    url = {http://dx.doi.org10.1093/bioinformatics/btp450},
  }